Iowa County was formed on February 17, 1843. It was named for the Iowa River, which flows through the county.
The first courthouse was a log cabin built in 1847. This was rented by the county until 1850 when a second courthouse was completed. In 1861 construction of a third courthouse was begun. The current courthouse was built in 1892 after the county had outgrown the previous one.
Iowa County is home to the Amana Colonies, a group of settlements of German Pietists, comprising seven villages. Calling themselves the Ebenezer Society or the Community of True Inspiration (German: die Gemeinde der wahren Inspiration), they first settled in New York state near Buffalo in what is now West Seneca. However, in order to live out their beliefs in more isolated surroundings they moved west, to Iowa County in 1855, living a communal life until the mid-1930s. Today, Amana is a major tourist attraction known mainly for its restaurants and craft shops, and the colonies as a whole have been listed as a National Historic Landmark since 1965.